I had a similar experience with my A4000D about a year ago after not using it for quite some time; also with a Cybervision 64/3D. My system is a little different though, a WarpEngine 040 and X-Surf instead of the cpu/network card combination that you have. I also have 3.2 ROMs but the problem existed with the previous 3.1 ROMs. However, the problem was similar. No matter what I tried, I could not get the Cybervision to 'work', meaning disply video. It was only recognized in the early start-up if it was in the lowest slot. Even when placed there, it was not recognized by P96 (I have the latest P96 version). The X-surf was recognized in all slots, but was only functional in the lowest slot.
I sent the machine to a repair shop for motherboard diagnostics. A few traces due to previous battery damage were repaired and all the motherboard caps were replaced. I even removed the WarpEngine and tried with the original 030 card. I also tried several other ZII cards. All to no avail.
After spending a great deal of time with this, I decided to take a chance and buy a brand new daughter card. I was pleasantly surprised that you can still buy these reproduction cards. Problem solved. I think the operative phrase here was "take a chance". I don't know anyone with an Amiga any more and I didn't seem to have any other options. Luckily for me it worked.
